My guess has something to do with the port side battery. I'm just guessing, though. Could have something to do with the port side magneto too. I would have to refer to a repair manual, which I don't have.

My MPEM has a sticker on it, that shows what you are talking about. There is a fuse for each engines charging system. There could have been something wrong with yours, hence the fuse being removed.

Thats gonna be a toughy..... Could be the magneto, battery switch shorted, or the MPEM itself. Connect a 12V test lamp between the battery ground cable and the negative post of the battery. The lamp should glow brightly. Start by taking the wire off the starter on that engine. If the light goes out, you found your short. If not, reconnect the wire. So on and so forth until you find what makes the light go out. Be sure the engine compartment is well vented before you start this process. Don't want any sparks in there with fuel vapors.....

Well, I got the new carbs installed and both engines start up and rev ok, but the real test is in the water.

Still no word from the seller. I filed a claim with my credit card company, so I might get my $400 deposit back, plus eBay's insurance might give me $200. That would cover most of the cost of getting back up and running. I have already dumped almost a grand into the boat and the trailer, and I haven't even transfered the title or registered it yet.

As for the MPEM, it is a Multi Purpose Electronic Module. Not sure what it does exactly, but I guess it is not required to run the boat, because the engines start fine without the fuse.

Well, at least maybe you won't have to eat the cost of the carbs.
You are correct in your name of the MPEM, but it IS required to run the engines. It has ALL of the ignition components, charging system electronics, sensors and such contained inside- potted in whatever it is they pot electronics in. With the fuse out, the only thing I see happening is the battery maintained by that engines charging system may not charge. There is a way to convert to just one battery, but I will have to find where I read that again.

No, what I'm saying is that one battery should not charge IF, in fact that was the STARBOARD SUPPLY fuse that was blowing . You may want to pose the question to the dealer as to what that blown fuse actually controls.